Domestication of plants and animals promoted humanity's transition from nomadic to sedentary lifestyles, demographic expansion, and the emergence of civilizations. In contrast to the well-documented successes of crop and livestock breeding, processes of microbe domestication remain obscure, despite the importance of microbes to the production of food, beverages, and biofuels. Lager-beer, first brewed in the 15th century, employs an allotetraploid hybrid yeast, Saccharomyces pastorianus (syn. Saccharomyces carlsbergensis), a domesticated species created by the fusion of a Saccharomyces cerevisiae ale-yeast with an unknown cryotolerant Saccharomyces species. We report the isolation of that species and designate it Saccharomyces eubayanus sp. nov. because of its resemblance to Saccharomyces bayanus (a complex hybrid of S. eubayanus, Saccharomyces uvarum, and S. cerevisiae found only in the brewing environment). Individuals from populations of S. eubayanus and its sister species, S. uvarum, exist in apparent sympatry in Nothofagus (Southern beech) forests in Patagonia, but are isolated genetically through intrinsic postzygotic barriers, and ecologically through host-preference. The draft genome sequence of S. eubayanus is 99.5% identical to the non-S. cerevisiae portion of the S. pastorianus genome sequence and suggests specific changes in sugar and sulfite metabolism that were crucial for domestication in the lager-brewing environment. This study shows that combining microbial ecology with comparative genomics facilitates the discovery and preservation of wild genetic stocks of domesticated microbes to trace their history, identify genetic changes, and suggest paths to further industrial improvement.

https://www.pnas.org/content/pnas/108/35/14539.full.pdf

Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast

Eating and Healing is aimed at exploring the idea that food can heal. The underlying argument of the volume is that, around the world, indigenous and rural people do not separate food and medicine, but rather consider them in a continuum. From the use in Spain of herbal teas as digestive beverages, to the antioxidant properties of Tibetan foods, we learn that the continuum concept is not unique to a single culture, but a common way in which humans use the natural environment. The various chapters of the volume describe a range of wild and semi-domesticated foods that traditionally have been used both as food and medicine. Although most chapters focus on the use of wild and semi-domesticated plants, the consumption of other foods (i.e., fish, mushrooms, seaweed) suggests that the overlapping nature of food and medicine is not particular to the plant kingdom, but a common way of conceptualizing. The publication of this volume is timely. The book appears at a moment in which the use of food as medicine is gaining attention among the general public in Western society. The volume, however, presents a refreshing perspective of the link between food intake and health. While medical doctors recommend the intake of dietary supplements and food scientists work to develop new “miraculous” foods (such as the golden rice) containing the nutrients lacking in many diets, this book is a call to go back to the essentials, to look at the local resources around us, and to consider the cultural context interwoven with the consumption of foods and medicines. As a whole, however, the volume does not present an overly optimistic and simplistic approach. Throughout the book, different authors point at three potential caveats of generalizing the ingestion of traditional foods as medicines. First, plants that are highly nutritious also have the potential to be highly toxic, so it is not possible to generalize their consumption without further inspection. Second, the eating of traditional foods and medicines is culturally prescribed and their intake disregarding the cultural system associated to them can result in a loss of effectiveness. Last, promoting the consumption of wild foods as medicines can increase the demand of those foods with potential pernicious effects on their sustainable use because of overextraction. By addressing the interface between food, medicine, and culture, Eating and Healing fills an important gap in ethnobiological research. The volume, however, would have benefited from including more quantitative contributions testing the various hypotheses presented. For example, quantitative data should allow researchers to test whether, in fact, people maintaining traditional diets enjoy better health. Future studies on the topic would benefit from using quantitative methods to test the relations between food and medicine. Victoria Reyes-García Institut de Ciencia i Tecnologia Ambiental Universitat Autonoma de Barcelona 08193 Bellaterra (Barcelona), Spain Victoria.Reyes@uab.es

First Farmers: The Origins of Agricultural Societies

The ever-expanding diversity of porcine reproductive and respiratory syndrome virus

Modern genetics, ecology and archaeology are combined to reconstruct the domestication and diversification of rice. Early rice cultivation followed two pathways towards domestication in India and China, with selection for domestication traits in early Yangtze japonica and a non-domestication feedback system inferred for ‘proto-indica’. The protracted domestication process finished around 6,500–6,000 years ago in China and about two millennia later in India, when hybridization with Chinese rice took place. Subsequently farming populations grew and expanded by migration and incorporation of pre-existing populations. These expansions can be linked to hypothetical language family dispersal models, including dispersal from China southwards by the Sino-Tibetan and Austronesian groups. In South Asia much dispersal of rice took place after Indo-Aryan and Dravidian speakers adopted rice from speakers of lost languages of northern India.

/pdf/pathways-to-asian-civilizations-tracing-the-origins-and-17sh736yi9.pdf

Pathways to Asian Civilizations: Tracing the Origins and Spread of Rice and Rice Cultures

Domestic pigs have evolved genetic adaptations to their local environmental conditions, such as cold and hot climates. We sequenced the genomes of 69 pigs from 15 geographically divergent locations in China and detected 41 million variants, of which 21 million were absent from the dbSNP database. In a genome-wide scan, we identified a set of loci that likely have a role in regional adaptations to high- and low-latitude environments within China. Intriguingly, we found an exceptionally large (14-Mb) region with a low recombination rate on the X chromosome that appears to have two distinct haplotypes in the high- and low-latitude populations, possibly underlying their adaptation to cold and hot environments, respectively. Surprisingly, the adaptive sweep in the high-latitude regions has acted on DNA that might have been introgressed from an extinct Sus species. Our findings provide new insights into the evolutionary history of pigs and the role of introgression in adaptation.

Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing.

The establishment of agricultural economies based upon domestic animals began independently in many parts of the world and led to both increases in human population size and the migration of people carrying domestic plants and animals. The precise circumstances of the earliest phases of these events remain mysterious given their antiquity and the fact that subsequent waves of migrants have often replaced the first. Through the use of more than 1,500 modern (including 151 previously uncharacterized specimens) and 18 ancient (representing six East Asian archeological sites) pig (Sus scrofa) DNA sequences sampled across East Asia, we provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. Although the Chinese case for independent pig domestication is supported by both genetic and archaeological evidence, we discuss five additional (and possibly) independent domestications of indigenous wild boar populations: one in India, three in peninsular Southeast Asia, and one off the coast of Taiwan. Collectively, we refer to these instances as “cryptic domestication,” given the current lack of corroborating archaeological evidence. In addition, we demonstrate the existence of numerous populations of genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East.

/pdf/patterns-of-east-asian-pig-domestication-migration-and-5a88vyu95w.pdf

Qipeng Fan

Papers

Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA